Empty Folders With Vanishing Files Mostly Documents

Over the years I've tried to save all my documents. This means that they have been copied from folder to folder and computer to computer (whatever was before Windows 95) probably mostly through external storage. However, some of these were saved directly to the 2nd internal hard drive D: of Windows 8 may be included, but I'm not certain.

I believe all of the folders are present, most of which are identified by date. However, many of the folders are completely empty. I cannot see a pattern as to which folders. This seems to involve mostly older folders, (and this may mean that it is more likely that they have been through a USB device) but not all of the older folders are empty. More recent ones are also empty. Otherwise, I cannot identify any specific documents, only that large numbers of folders are empty.